ATAC-Seq/ RNA-Seq (PND15 vs Adultys): Diff accessible peaks and diff exp genes

Library

library(plotly)
library(SummarizedExperiment)

Data

load("./input/atac_diff_chromatin_accessibility.RData")
load("./input/limma_SC_Controls.RData")

dea <- dea.limma$`PND15 vs Adult`
anno <- data.frame(data@metadata$annotation@anno, stringsAsFactors = F)
dar <- data.frame(rowData(data), stringsAsFactors = F)[, -c(2:6)]
dar <- merge(anno, dar, all.y = TRUE)

Map with Genes

dea.map <- dea[abs(dea$logFC) >= 1 & dea$adj.P.Val <= 0.05, ]
colnames(dea.map)[2:ncol(dea.map)] <- paste("DEA", colnames(dea.map)[2:ncol(dea.map)], sep = "_")

dar.map <- dar[abs(dar$logFC) >= 1 & dar$qvalue <= 0.05, ]

tab <- merge(dar.map, dea.map, by.x = "SYMBOL", by.y = "Genes")
tab.promoter <- tab[tab$annotation == "Promoter", ]

Save table

writexl::write_xlsx(tab, "./output/dea_genes_mapped_to_diff_acc.xlsx", col_names = T, format_headers = T)

Plot for promoters

plot_ly(
  data = tab.promoter, x = ~DEA_logFC, y = ~logFC,
  marker = list(size = 5, color = "blue"),
  text = ~ paste(
    "Gene: ", SYMBOL,
    "<br>Name: ", GENENAME,
    "<br>DA logFC: ", logFC,
    "<br>DA FDR: ", qvalue,
    "<br>DE logFC: ", DEA_logFC,
    "<br>DE FDR: ", DEA_adj.P.Val
  ),
  hoverinfo = "text"
) %>%
  layout(
    title = "Differential accessible regions (promoters) vs differentially expressed genes",
    yaxis = list(title = "logFC: Differential Accessibility (DA)"),
    xaxis = list(title = "logFC: Differential Expression (DE)")
  )

SessionInfo

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.1 (2019-07-05)
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##  system   x86_64, linux-gnu           
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##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2019-11-29                  
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Deepak Tanwar

Created on: 2019-11-29
Updated on: 2019-11-29